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  <meta name="description" content="功能gomonitor agsTask &lt;arguments&gt; 投递的项目有以下feature  agsTask的主要功能是把一个project内的所有任务整体作为一个workflow通过argo软件投递到kubernetes 执行投递命令会返回一个argoID，通过ags get argoID能够获得项目workflow的状态信息  通过此模式投递的project能够通过gomoni">
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                <h1 id="功能" class="article-heading"><a href="#功能" class="headerlink" title="功能"></a>功能<a class="article-anchor" href="#功能" aria-hidden="true"></a></h1><p><code>gomonitor agsTask &lt;arguments&gt;</code> 投递的项目有以下feature</p>
<ul>
<li>agsTask的主要功能是把一个project内的所有任务整体作为一个workflow通过argo软件投递到kubernetes</li>
<li>执行投递命令会返回一个argoID，通过<code>ags get argoID</code>能够获得项目workflow的状态信息</li>
<li> 通过此模式投递的project能够通过<a target="_blank" rel="noopener external nofollow noreferrer" href="https://gitlab.com/seqyuan/gomonitor/wikis/stat" title="stat"><code>gomonitor stat</code></a>命令查询项目的状态，获得项目所在gomonitor数据库的Id号</li>
<li> 通过此模式投递的project能够通过<code>gomonitor stat -p Id</code>命令查询特定项目的详细状态，主要包括 project内各模块的依赖关系、project内各模块的运行状态、项目workflow的argoID、项目的起始时间、结束时间以及项目信息的sqlite3数据库</li>
</ul>
<h1 id="Arguments" class="article-heading"><a href="#Arguments" class="headerlink" title="Arguments"></a>Arguments<a class="article-anchor" href="#Arguments" aria-hidden="true"></a></h1><figure class="highlight shell"><table><tr><td class="code"><pre><span class="line">Arguments:</span><br><span class="line"></span><br><span class="line">  -i  --main_ini_depend  main dependence file</span><br><span class="line">  -p  --project_name     Project name. Default: workflow</span><br><span class="line">  -t  --project_type     project type. Default: None</span><br><span class="line">  -b  --Project_batch    project type. Default: None</span><br><span class="line">  -l  --last_module      Last run module name. Default: --</span><br><span class="line">  -e  --env              Calculation queue. Default: idc_physical</span><br><span class="line">  -f  --finish_mark      Using the strings specified by -s option at the end of files</span><br><span class="line">		           0  .e files</span><br><span class="line">		           1  Using .sign files.</span><br><span class="line">		           2  Do not check.</span><br><span class="line">		           3  Using the strings specified by -s option at the end of .o files.</span><br><span class="line">                           Default: 1</span><br><span class="line">  -s  --finish_str       Finish string for -f option. Default:</span><br><span class="line">                         Still_waters_run_deep</span><br><span class="line">  -m  --addmode          Operation mode for resubmitting the same project</span><br><span class="line">		           0  Resubmit those did not successfully finished, and jobs depend on them.</span><br><span class="line">		           1  Resubmit scripts that were added or modified after execution, and jobs depend on them.</span><br><span class="line">		           2  Resubmit all jobs. No matter successful or not.. Default: 0</span><br><span class="line">  -h  --help             Print help information</span><br><span class="line"></span><br></pre></td></tr></table></figure>
<h1 id="Arguments，gomonitor-agsTask各参数说明" class="article-heading"><a href="#Arguments，gomonitor-agsTask各参数说明" class="headerlink" title="Arguments，gomonitor agsTask各参数说明"></a>Arguments，gomonitor agsTask各参数说明<a class="article-anchor" href="#Arguments，gomonitor-agsTask各参数说明" aria-hidden="true"></a></h1><h2 id="i" class="article-heading"><a href="#i" class="headerlink" title="-i"></a><code>-i</code><a class="article-anchor" href="#i" aria-hidden="true"></a></h2><p>A text file，<code>-i</code>参数是一个两列的文本文件，<code>tab</code>隔开，用于描述project中各任务之间的运行逻辑</p>
<p>第一列为第二列运行的前提条件，第二列可以为空。</p>
<p>此文件可由最新k8s版的generate_pipeline产生，也可自己写脚本生成，参考Hi-C流程中模块主脚本的写法。<code>-i</code>参数的文件示例如下：</p>
<table>
<thead>
<tr>
<th>/abspath/shell/1-0-cut-raw.ini</th>
<th>/abspath/shell/2-0-filter.ini</th>
</tr>
</thead>
<tbody><tr>
<td>/abspath/shell/2-0-filter.ini</td>
<td>/abspath/shell/3-0-stat-dup-poly.ini</td>
</tr>
<tr>
<td>/abspath/shell/2-0-filter.ini</td>
<td>/abspath/shell/3-1-nt-blastn.ini</td>
</tr>
<tr>
<td>/abspath/shell/3-1-nt-blastn.ini</td>
<td>/abspath/shell/3-2-nt-stat.ini</td>
</tr>
<tr>
<td>/abspath/shell/2-0-filter.ini</td>
<td>/abspath/shell/3-2-nt-stat.ini</td>
</tr>
<tr>
<td>/abspath/shell/3-0-stat-dup-poly.ini</td>
<td>/abspath/shell/4-0-stat.ini</td>
</tr>
<tr>
<td>/abspath/shell/4-0-stat.ini</td>
<td>/abspath/shell/5-0-md5.ini</td>
</tr>
<tr>
<td>/abspath/shell/5-0-md5.ini</td>
<td>/abspath/shell/6-0-feedback.ini</td>
</tr>
<tr>
<td>/abspath/shell/3-2-nt-stat.ini</td>
<td>/abspath/shell/6-1-nt-feedback.ini</td>
</tr>
<tr>
<td>/abspath/shell/6-0-feedback.ini</td>
<td>/abspath/shell/6-1-nt-feedback.ini</td>
</tr>
<tr>
<td>/abspath/shell/5-0-md5.ini</td>
<td>/abspath/shell/6-1-nt-feedback.ini</td>
</tr>
<tr>
<td>/abspath/shell/3-2-nt-stat.ini</td>
<td>/abspath/shell/7-0-filter-result.ini</td>
</tr>
<tr>
<td>/abspath/shell/3-0-stat-dup-poly.ini</td>
<td>/abspath/shell/7-0-filter-result.ini</td>
</tr>
<tr>
<td>/abspath/shell/6-0-feedback.ini</td>
<td>/abspath/shell/7-0-filter-result.ini</td>
</tr>
<tr>
<td>/abspath/shell/7-0-filter-result.ini</td>
<td>/abspath/shell/8-0-md5-all.ini</td>
</tr>
<tr>
<td>/abspath/shell/7-0-filter-result.ini</td>
<td>/abspath/shell/8-1-html2pdf.ini</td>
</tr>
<tr>
<td>/abspath/shell/8-1-html2pdf.ini</td>
<td>/abspath/shell/8-2-send-report.ini</td>
</tr>
<tr>
<td>/abspath/shell/7-0-filter-result.ini</td>
<td>/abspath/shell/8-2-send-report.ini</td>
</tr>
</tbody></table>
<p><code>-i</code>两列均为要执行任务的配置文件，采用标准的ini格式，格式示例如下所示：</p>
<h3 id="pod-config-example" class="article-heading"><a href="#pod-config-example" class="headerlink" title="pod config example"></a><strong><code>pod config example</code></strong><a class="article-anchor" href="#pod-config-example" aria-hidden="true"></a></h3><blockquote>
<p>1-0-cut-raw.ini </p>
</blockquote>
<figure class="highlight shell"><table><tr><td class="code"><pre><span class="line">[templetes]</span><br><span class="line">pod_name = 1-0-cut-raw</span><br><span class="line">module = cut-raw</span><br><span class="line">template = cut-raw</span><br><span class="line">imagePullSecrets = registry-read-only-key-bj</span><br><span class="line"></span><br><span class="line">[requests]</span><br><span class="line">memory = 5</span><br><span class="line">cpu = 6</span><br><span class="line"></span><br><span class="line">[limits]</span><br><span class="line">memory = 7.5</span><br><span class="line">cpu = 6</span><br><span class="line"></span><br><span class="line">[container]</span><br><span class="line">image = registry-vpc.cn-beijing.aliyuncs.com/annoroad/centos-python_perl_r:v0.1</span><br><span class="line">command = [sh ,-c]</span><br><span class="line">args = /home/zanyuan/bin/example/agsTask_test3/shell/shell//1-0-cut-raw/1-0-cut-raw.sh</span><br><span class="line">lines = 4</span><br><span class="line"></span><br><span class="line">[volumeMounts]</span><br><span class="line">sge = /data1|x400.bjannoroad.local|/annoroad/data1</span><br><span class="line">workdir = /cloud|x400.bjannoroad.local|/annoroad/cloud</span><br><span class="line">home = /cloud_home|x400.bjannoroad.local|/home</span><br><span class="line"></span><br><span class="line">[NodeSelector]</span><br><span class="line"></span><br></pre></td></tr></table></figure>
<blockquote>
<p><code>单个任务的配置文件格式说明</code>，同样适用于<a target="_blank" rel="noopener external nofollow noreferrer" href="https://gitlab.com/seqyuan/gomonitor/wikis/submit" title="submit"><code>gomonitor submit</code></a>命令</p>
</blockquote>
<ul>
<li><input disabled type="checkbox"> <strong>templetes</strong> <ol>
<li>pod_name: job的名称，请保持其在<code>-i</code>中的唯一性</li>
<li>module: job所在的模块名称，一个模块可能包含多个job</li>
<li>template: 为了减少投递到argo时配置文件的大小，设置此项，例如比对步骤不同样品采用相同的template名称</li>
<li>imagePullSecrets: docker镜像仓库的key，找镜像仓库管理员获得，注意义乌与北京仓库此项应为不同值</li>
</ol>
</li>
<li><input disabled type="checkbox"> <strong>requests</strong> <ol>
<li>memory: job需要的内存大小</li>
<li>cpu: job需要的cpu大小</li>
</ol>
</li>
<li><input disabled type="checkbox"> <strong>limits</strong> <ol>
<li>memory: job需要的内存限制，超出此限制会被k8s系统删除</li>
<li>cpu: job需要的cpu限制，超出此限制会被k8s系统删除</li>
</ol>
</li>
<li><input disabled type="checkbox"> <strong>container</strong> <ol>
<li>image: job启动容器需要的的镜像地址</li>
<li>command: 此项为固定设置值[sh ,-c]</li>
<li>args: 此项可以是1个脚本的绝对路径，表示此job要执行的脚本</li>
<li>lines: 此项为数字整型，此项可设置为空，表示<code>args</code>设置的脚本整体按内容的顺序执行；设置其他非0整型N，则<strong>args</strong>设置的脚本会按照每N行1个单位，并行的去执行其中内容，详见<a target="_blank" rel="noopener external nofollow noreferrer" href="https://gitlab.com/seqyuan/gomonitor/wikis/submit" title="submit"><code>gomonitor submit</code></a>中的example</li>
</ol>
</li>
<li><input disabled type="checkbox"> <strong>volumeMounts</strong>，此项表示执行此job要挂载的路径，此section内的key与value不固定，可以有多个key value，表示挂载多个目录。key: This must match the Name of a Volume，value用两个”|”分割成3项<ol>
<li>value的第1项：Volume’s name, Must be a DNS_LABEL</li>
<li>value的第2项：Server, server is the hostname or IP address of the NFS server</li>
<li>value的第3项：Path, path that is exported by the NFS server.</li>
</ol>
</li>
<li><input disabled type="checkbox"> <strong>NodeSelector</strong>，此项表示job投递需要的计算资源label信息，可以设置为空，或者多个键值对，推荐设置1个键值对或者为空，为空时表示使用阿里云弹性资源，Selector which must match a node’s labels for the pod to be scheduled on that node。可选项可联系集群管理员确定，目前可选项<figure class="highlight plain"><table><tr><td class="code"><pre><span class="line">北京：</span><br><span class="line">       node: idc_physical</span><br><span class="line">       network &#x3D; internet ，联网节点</span><br><span class="line">义乌：</span><br><span class="line">       env &#x3D; idc_physical</span><br><span class="line">       network &#x3D; internet ，联网节点</span><br></pre></td></tr></table></figure>
<h2 id="l" class="article-heading"><a href="#l" class="headerlink" title="-l"></a><code>-l</code><a class="article-anchor" href="#l" aria-hidden="true"></a></h2>Last module, from the pod <code>templetes</code> config section <code>module</code> option, if the module in the <code>-i</code> depend list, the pod in the module would exec at last no mater which pod its depend </li>
</ul>
<p>-l参数可以不设置，或者指定为<code>-i</code>参数中各配置文件的某个module，用于表示这个module内的job在执行完成其他module之后再执行。一般情况下我们会把生产结题报告的report module放到最后去执行，report module中的各job可以保持DAG关系。</p>
<h1 id="example，使用示例" class="article-heading"><a href="#example，使用示例" class="headerlink" title="example，使用示例"></a>example，使用示例<a class="article-anchor" href="#example，使用示例" aria-hidden="true"></a></h1><p>以下为使用<code>gomonitor agsTask</code>的示例命令</p>
<blockquote>
<p> <code>gomonitor agsTask -i /abspath/all.txt -p PM-BJ181119-15-test -t FILTER </code></p>
</blockquote>
<p>执行以上命令后会返回project投递到argo的AgsID<br><code>AgsID: pm-bj181119-15-test3-filterxf7sg</code><br>可使用<code>ags get AgsID</code>命令查看workflow的状态，也可以通过<code>ags get AgsID --metrics</code>命令查看workflow的资源消耗情况</p>
<blockquote>
<p><code>ags get pm-bj181119-15-test3-filterxf7sg </code>，执行此命令后得到的信息如下所示：</p>
</blockquote>
<figure class="highlight shell"><table><tr><td class="code"><pre><span class="line">Name:                pm-bj181119-15-test3-filterxf7sg</span><br><span class="line">Namespace:           zanyuan</span><br><span class="line">ServiceAccount:      default</span><br><span class="line">Status:              Succeeded</span><br><span class="line">Created:             Wed Jul 10 13:58:21 +0800 (1 day ago)</span><br><span class="line">Started:             Wed Jul 10 13:58:21 +0800 (1 day ago)</span><br><span class="line">Finished:            Wed Jul 10 15:03:34 +0800 (1 day ago)</span><br><span class="line">Duration:            1 hour 5 minutes</span><br><span class="line"></span><br><span class="line">STEP                                        PODNAME                                      DURATION  MESSAGE</span><br><span class="line"> ✔ pm-bj181119-15-test3-filterxf7sg                                                                </span><br><span class="line"> ├-✔ 1-0-cut-raw                                                                                   </span><br><span class="line"> | ├-·-✔ cut-raw-1-0-cut-raw-1              pm-bj181119-15-test3-filterxf7sg-3518185999  16s       </span><br><span class="line"> | | ├-✔ cut-raw-1-0-cut-raw-2              pm-bj181119-15-test3-filterxf7sg-3534963618  11s       </span><br><span class="line"> | | ├-✔ cut-raw-1-0-cut-raw-3              pm-bj181119-15-test3-filterxf7sg-3551741237  9s        </span><br><span class="line"> | | ├-✔ cut-raw-1-0-cut-raw-4              pm-bj181119-15-test3-filterxf7sg-3434297904  9s        </span><br><span class="line"> | | ├-✔ cut-raw-1-0-cut-raw-5              pm-bj181119-15-test3-filterxf7sg-3451075523  9s        </span><br><span class="line"> | | └-✔ cut-raw-1-0-cut-raw-6              pm-bj181119-15-test3-filterxf7sg-3467853142  24s       </span><br><span class="line"> | └---✔ sign                               pm-bj181119-15-test3-filterxf7sg-3026636147  3s        </span><br><span class="line"> ├-✔ 2-0-filter                                                                                    </span><br><span class="line"> | ├-·-✔ filter-2-0-filter-1                pm-bj181119-15-test3-filterxf7sg-3847606146  15m       </span><br><span class="line"> | | ├-✔ filter-2-0-filter-2                pm-bj181119-15-test3-filterxf7sg-3830828527  12m       </span><br><span class="line"> | | ├-✔ filter-2-0-filter-3                pm-bj181119-15-test3-filterxf7sg-3814050908  12m       </span><br><span class="line"> | | ├-✔ filter-2-0-filter-4                pm-bj181119-15-test3-filterxf7sg-3797273289  13m       </span><br><span class="line"> | | ├-✔ filter-2-0-filter-5                pm-bj181119-15-test3-filterxf7sg-3780495670  14m       </span><br><span class="line"> | | └-✔ filter-2-0-filter-6                pm-bj181119-15-test3-filterxf7sg-3763718051  15m       </span><br><span class="line"> | └---✔ sign                               pm-bj181119-15-test3-filterxf7sg-4225146849  12s       </span><br><span class="line"> ├-✔ 3-0-stat-dup-poly                                                                             </span><br><span class="line"> | ├-·-✔ stat-dup-poly-3-0-stat-dup-poly-1  pm-bj181119-15-test3-filterxf7sg-3233371467  3m        </span><br><span class="line"> | | ├-✔ stat-dup-poly-3-0-stat-dup-poly-2  pm-bj181119-15-test3-filterxf7sg-3250149086  2m        </span><br><span class="line"> | | ├-✔ stat-dup-poly-3-0-stat-dup-poly-3  pm-bj181119-15-test3-filterxf7sg-3266926705  2m        </span><br><span class="line"> | | ├-✔ stat-dup-poly-3-0-stat-dup-poly-4  pm-bj181119-15-test3-filterxf7sg-3283704324  3m        </span><br><span class="line"> | | ├-✔ stat-dup-poly-3-0-stat-dup-poly-5  pm-bj181119-15-test3-filterxf7sg-3300481943  3m        </span><br><span class="line"> | | └-✔ stat-dup-poly-3-0-stat-dup-poly-6  pm-bj181119-15-test3-filterxf7sg-3317259562  3m        </span><br><span class="line"> | └---✔ sign                               pm-bj181119-15-test3-filterxf7sg-44753841    3s        </span><br><span class="line"> ├-✔ 3-1-nt-blastn                                                                                 </span><br><span class="line"> | ├-·-✔ nt-blastn-3-1-nt-blastn-1          pm-bj181119-15-test3-filterxf7sg-3658812387  29m       </span><br><span class="line"> | | ├-✔ nt-blastn-3-1-nt-blastn-2          pm-bj181119-15-test3-filterxf7sg-3675590006  27m       </span><br><span class="line"> | | ├-✔ nt-blastn-3-1-nt-blastn-3          pm-bj181119-15-test3-filterxf7sg-3692367625  33m       </span><br><span class="line"> | | ├-✔ nt-blastn-3-1-nt-blastn-4          pm-bj181119-15-test3-filterxf7sg-3709145244  30m       </span><br><span class="line"> | | ├-✔ nt-blastn-3-1-nt-blastn-5          pm-bj181119-15-test3-filterxf7sg-3725922863  28m       </span><br><span class="line"> | | └-✔ nt-blastn-3-1-nt-blastn-6          pm-bj181119-15-test3-filterxf7sg-3742700482  31m       </span><br><span class="line"> | └---✔ sign                               pm-bj181119-15-test3-filterxf7sg-3715854636  9s        </span><br><span class="line"> ├-✔ 4-0-stat                                                                                      </span><br><span class="line"> | ├---✔ stat-4-0-stat-1                    pm-bj181119-15-test3-filterxf7sg-3029662790  14s       </span><br><span class="line"> | └---✔ sign                               pm-bj181119-15-test3-filterxf7sg-1289608023  9s        </span><br><span class="line"> ├-✔ 5-0-md5                                                                                       </span><br><span class="line"> | ├---✔ md5-5-0-md5-1                      pm-bj181119-15-test3-filterxf7sg-4151038802  3m        </span><br><span class="line"> | └---✔ sign                               pm-bj181119-15-test3-filterxf7sg-2395077828  8s        </span><br><span class="line"> ├-✔ 6-0-feedback                                                                                  </span><br><span class="line"> | ├---✔ feedback-6-0-feedback-1            pm-bj181119-15-test3-filterxf7sg-2544232295  1m        </span><br><span class="line"> | └---✔ sign                               pm-bj181119-15-test3-filterxf7sg-1221889880  10s       </span><br><span class="line"> ├-✔ 3-2-nt-stat                                                                                   </span><br><span class="line"> | ├-·-✔ nt-stat-3-2-nt-stat-1              pm-bj181119-15-test3-filterxf7sg-2204345279  11m       </span><br><span class="line"> | | ├-✔ nt-stat-3-2-nt-stat-2              pm-bj181119-15-test3-filterxf7sg-2221122898  11m       </span><br><span class="line"> | | ├-✔ nt-stat-3-2-nt-stat-3              pm-bj181119-15-test3-filterxf7sg-2237900517  11m       </span><br><span class="line"> | | ├-✔ nt-stat-3-2-nt-stat-4              pm-bj181119-15-test3-filterxf7sg-2120457184  11m       </span><br><span class="line"> | | ├-✔ nt-stat-3-2-nt-stat-5              pm-bj181119-15-test3-filterxf7sg-2137234803  11m       </span><br><span class="line"> | | └-✔ nt-stat-3-2-nt-stat-6              pm-bj181119-15-test3-filterxf7sg-2154012422  11m       </span><br><span class="line"> | └---✔ sign                               pm-bj181119-15-test3-filterxf7sg-3533206747  10s       </span><br><span class="line"> ├-✔ 6-1-nt-feedback                                                                               </span><br><span class="line"> | ├---✔ nt-feedback-6-1-nt-feedback-1      pm-bj181119-15-test3-filterxf7sg-1992993100  1m        </span><br><span class="line"> | └---✔ sign                               pm-bj181119-15-test3-filterxf7sg-3978405544  3s        </span><br><span class="line"> ├-✔ 7-0-filter-result                                                                             </span><br><span class="line"> | ├---✔ filter-result-7-0-filter-result-1  pm-bj181119-15-test3-filterxf7sg-2721433578  1m        </span><br><span class="line"> | └---✔ sign                               pm-bj181119-15-test3-filterxf7sg-3170040650  9s        </span><br><span class="line"> ├-✔ 8-1-html2pdf                                                                                  </span><br><span class="line"> | ├---✔ html2pdf-8-1-html2pdf-1            pm-bj181119-15-test3-filterxf7sg-2744460583  8s        </span><br><span class="line"> | └---✔ sign                               pm-bj181119-15-test3-filterxf7sg-2346318697  3s        </span><br><span class="line"> ├-✔ 8-0-md5-all                                                                                   </span><br><span class="line"> | ├---✔ md5-all-8-0-md5-all-1              pm-bj181119-15-test3-filterxf7sg-428320106   1m        </span><br><span class="line"> | └---✔ sign                               pm-bj181119-15-test3-filterxf7sg-1719563473  3s        </span><br><span class="line"> └-✔ 8-2-send-report                                                                               </span><br><span class="line">   ├---✔ send-report-8-2-send-report-1      pm-bj181119-15-test3-filterxf7sg-1424952785  1m        </span><br><span class="line">   └---✔ sign                               pm-bj181119-15-test3-filterxf7sg-2624527654  2s</span><br></pre></td></tr></table></figure>
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